tbuckley/cabot-search huggingface dataset:
In-ear infrasonic hemodynography with a digital health device for cardiovascular monitoring using the human audiome
Authors: Francis Roosevelt Gilliam, Robert Ciesielski, Karlen Shahinyan, Pratistha Shakya, John Cunsolo, Jal Mahendra Panchal, Bartlomiej Król-Józaga, Monika Król, Olivia Kierul, Charles Bridges, Christine Shen, Carly E. Waldman, Martin Ring, Tomasz Szepieniec, Anna Barnacka, Sanjeev P. Bhavnani
Journal: npj Digital Medicine (2022)

Human bodily mechanisms and functions produce low-frequency vibrations. Our ability to perceive these vibrations is limited by our range of hearing. However, in-ear infrasonic hemodynography (IH) can measure low-frequency vibrations (<20 Hz) created by vital organs as an acoustic waveform. This is captured using a technology that can be embedded into wearable devices such as in-ear headphones. IH can acquire sound signals that travel within arteries, fluids, bones, and muscles in proximity to the ear canal, allowing for measurements of an individual's unique audiome. We describe the heart rate and heart rhythm results obtained in time-series analysis of the in-ear IH data taken simultaneously with ECG recordings in two dedicated clinical studies. We demonstrate a high correlation (r = 0.99) between IH and ECG acquired interbeat interval and heart rate measurements and show that IH can continuously monitor physiological changes in heart rate induced by various breathing exercises. We also show that IH can differentiate between atrial fibrillation and sinus rhythm with performance similar to ECG. The results represent a demonstration of IH capabilities to deliver accurate heart rate and heart rhythm measurements comparable to ECG, in a wearable form factor. The development of IH shows promise for monitoring acoustic imprints of the human body that will enable new real-time applications in cardiovascular health that are continuous and noninvasive.
A neurophenomenological approach to non-ordinary states of consciousness: hypnosis, meditation, and psychedelics
Authors: Christopher Timmermann, Prisca R. Bauer, Olivia Gosseries, Audrey Vanhaudenhuyse, Franz Vollenweider, Steven Laureys, Tania Singer, Elena Antonova, Antoine Lutz
Journal: Trends in Cognitive Sciences (2022)

No contemporary unifying framework has been provided for the study of non-ordinary states of consciousness (NSCs) despite increased interest in hypnosis, meditation, and psychedelics. NSCs induce shifts in experiential contents (what appears to the experiencer) and/or structure (how it appears). This can allow the investigation of the plastic and dynamic nature of experience from a multiscale perspective that includes mind, brain, body, and context. We propose a neurophenomenological (NP) approach to the study of NSCs which highlights their role as catalysts of transformation in clinical practice by refining our understanding of the relationships between experiential (subjective) and neural dynamics. We outline the ethical implications of the NP approach for standard conceptions of health and pathology as well as the crucial role of experience-based know-how in NSC-related research and application.
Different prognostic impact of recurrent gene mutations in chronic lymphocytic leukemia depending on IGHV gene somatic hypermutation status: a study by ERIC in HARMONY
Authors: Larry Mansouri, Birna Thorvaldsdottir, Lesley-Ann Sutton, Georgios Karakatsoulis, Manja Meggendorfer, Helen Parker, Ferran Nadeu, Christian Brieghel, Stamatia Laidou, Riccardo Moia, Davide Rossi, Mark Catherwood, Jana Kotaskova, Julio Delgado, Ana E. Rodríguez-Vicente, Rocío Benito, Gian Matteo Rigolin, Silvia Bonfiglio, Lydia Scarfo, Mattias Mattsson, Zadie Davis, Ajay Gogia, Lata Rani, Panagiotis Baliakas, Hassan Foroughi-Asl, Cecilia Jylhä, Aron Skaftason, Inmaculada Rapado, Fatima Miras, Joaquín Martinez-Lopez, Javier de la Serna, Jesús María Hernández Rivas, Patrick Thornton, María José Larráyoz, María José Calasanz, Viktória Fésüs, Zoltán Mátrai, Csaba Bödör, Karin E. Smedby, Blanca Espinet, Anna Puiggros, Ritu Gupta, Lars Bullinger, Francesc Bosch, Bárbara Tazón-Vega, Fanny Baran-Marszak, David Oscier, Florence Nguyen-Khac, Thorsten Zenz, Maria Jose Terol, Antonio Cuneo, María Hernández-Sánchez, Sarka Pospisilova, Ken Mills, Gianluca Gaidano, Carsten U. Niemann, Elias Campo, Jonathan C. Strefford, Paolo Ghia, Kostas Stamatopoulos, Richard Rosenquist
Journal: Leukemia (2022)

Recent evidence suggests that the prognostic impact of gene mutations in patients with chronic lymphocytic leukemia (CLL) may differ depending on the immunoglobulin heavy variable (IGHV) gene somatic hypermutation (SHM) status. In this study, we assessed the impact of nine recurrently mutated genes (BIRC3, EGR2, MYD88, NFKBIE, NOTCH1, POT1, SF3B1, TP53, and XPO1) in pre-treatment samples from 4580 patients with CLL, using time-to-first-treatment (TTFT) as the primary end-point in relation to IGHV gene SHM status. Mutations were detected in 1588 (34.7%) patients at frequencies ranging from 2.3-9.8% with mutations in NOTCH1 being the most frequent. In both univariate and multivariate analyses, mutations in all genes except MYD88 were associated with a significantly shorter TTFT. In multivariate analysis of Binet stage A patients, performed separately for IGHV-mutated (M-CLL) and unmutated CLL (U-CLL), a different spectrum of gene alterations independently predicted short TTFT within the two subgroups. While SF3B1 and XPO1 mutations were independent prognostic variables in both U-CLL and M-CLL, TP53, BIRC3 and EGR2 aberrations were significant predictors only in U-CLL, and NOTCH1 and NFKBIE only in M-CLL. Our findings underscore the need for a compartmentalized approach to identify high-risk patients, particularly among M-CLL patients, with potential implications for stratified management.
Modulation of NLRP3 inflammasomes activation contributes to improved survival and function of mesenchymal stromal cell spheroids
Authors: Duc-Vinh Pham, Prakash Shrestha, Thi-Kem Nguyen, Junhyeung Park, Mahesh Pandit, Jae-Hoon Chang, Soo Young Kim, Dong-Young Choi, Sung Soo Han, Inho Choi, Gyu Hwan Park, Jee-Heon Jeong, Pil-Hoon Park
Journal: Molecular Therapy (2022)

Mesenchymal stem cells (MSCs) are ubiquitous multipotent cells that exhibit significant therapeutic potentials in a variety of disorders. Nevertheless, their clinical efficacy is limited owing to poor survival, low rate of engraftment, and impaired potency upon transplantation. Spheroidal three-dimensional (3D) culture of MSCs (MSC3D) has been proven to better preserve their in vivo functional properties. However, the molecular mechanisms underlying the improvement in MSC function by spheroid formation are not clearly understood. NLRP3 inflammasomes, a key component of the innate immune system, have recently been shown to play a role in cell fate decision of MSCs. The present study examined the role of NLRP3 inflammasomes in the survival and potency of MSC spheroids. We found that MSC3D led to decreased activation of NLRP3 inflammasomes through alleviation of ER stress in an autophagy-dependent manner. Importantly, downregulation of NLRP3 inflammasomes signaling critically contributes to the enhanced survival rate in MSC3D through modulation of pyroptosis and apoptosis. The critical role of NLRP3 inflammasome suppression in the enhanced therapeutic efficacy of MSC spheroids was further confirmed in an in vivo mouse model of DSS-induced colitis. These findings suggest that 3D culture confers survival and functional advantages to MSCs by suppressing NLRP3 inflammasome activation. Mesenchymal stem cells (MSCs) are ubiquitous multipotent cells that exhibit significant therapeutic potentials in a variety of disorders. Nevertheless, their clinical efficacy is limited owing to poor survival, low rate of engraftment, and impaired potency upon transplantation. Spheroidal three-dimensional (3D) culture of MSCs (MSC3D) has been proven to better preserve their in vivo functional properties. However, the molecular mechanisms underlying the improvement in MSC function by spheroid formation are not clearly understood. NLRP3 inflammasomes, a key component of the innate immune system, have recently been shown to play a role in cell fate decision of MSCs. The present study examined the role of NLRP3 inflammasomes in the survival and potency of MSC spheroids. We found that MSC3D led to decreased activation of NLRP3 inflammasomes through alleviation of ER stress in an autophagy-dependent manner. Importantly, downregulation of NLRP3 inflammasomes signaling critically contributes to the enhanced survival rate in MSC3D through modulation of pyroptosis and apoptosis. The critical role of NLRP3 inflammasome suppression in the enhanced therapeutic efficacy of MSC spheroids was further confirmed in an in vivo mouse model of DSS-induced colitis. These findings suggest that 3D culture confers survival and functional advantages to MSCs by suppressing NLRP3 inflammasome activation.
A positive feedback circuit between RN7SK snRNA and m6A readers is essential for tumorigenesis
Authors: Xin Xu, Lifang Ma, Xiao Zhang, Susu Guo, Wanxin Guo, Yikun Wang, Shiyu Qiu, Xiaoting Tian, Yayou Miao, Yongchun Yu, Jiayi Wang
Journal: Molecular Therapy (2022)

N6-Methyladenosine (m6A) RNA modification, methylation at the N6 position of adenosine, plays critical roles in tumorigenesis. m6A readers recognize m6A modifications and thus act as key executors for the biological consequences of RNA methylation. However, knowledge about the regulatory mechanism(s) of m6A readers is extremely limited. In this study, RN7SK was identified as a small nuclear RNA that interacts with m6A readers. m6A readers recognized and facilitated secondary structure formation of m6A-modified RN7SK, which in turn prevented m6A reader mRNA degradation from exonucleases. Thus, a positive feedback circuit between RN7SK and m6A readers is established in tumor cells. From findings on the interaction with RN7SK, new m6A readers, such as EWS RNA binding protein 1 (EWSR1) and KH RNA binding domain containing, signal transduction-associated 1 (KHDRBS1), were identified and shown to boost Wnt/β-catenin signaling and tumorigenesis by suppressing translation of Cullin1 (CUL1). Moreover, several Food and Drug Administration-approved small molecules were demonstrated to reduce RN7SK expression and inhibit tumorigenesis. Together, these findings reveal a common regulatory mechanism of m6A readers and indicate that targeting RN7SK has strong potential for tumor treatment. N6-Methyladenosine (m6A) RNA modification, methylation at the N6 position of adenosine, plays critical roles in tumorigenesis. m6A readers recognize m6A modifications and thus act as key executors for the biological consequences of RNA methylation. However, knowledge about the regulatory mechanism(s) of m6A readers is extremely limited. In this study, RN7SK was identified as a small nuclear RNA that interacts with m6A readers. m6A readers recognized and facilitated secondary structure formation of m6A-modified RN7SK, which in turn prevented m6A reader mRNA degradation from exonucleases. Thus, a positive feedback circuit between RN7SK and m6A readers is established in tumor cells. From findings on the interaction with RN7SK, new m6A readers, such as EWS RNA binding protein 1 (EWSR1) and KH RNA binding domain containing, signal transduction-associated 1 (KHDRBS1), were identified and shown to boost Wnt/β-catenin signaling and tumorigenesis by suppressing translation of Cullin1 (CUL1). Moreover, several Food and Drug Administration-approved small molecules were demonstrated to reduce RN7SK expression and inhibit tumorigenesis. Together, these findings reveal a common regulatory mechanism of m6A readers and indicate that targeting RN7SK has strong potential for tumor treatment.
Inhalable neutralizing antibodies – promising approach to combating respiratory viral infections
Authors: Michael Y.T. Chow, Harry W. Pan, Han Cong Seow, Jenny K.W. Lam
Journal: Trends in Pharmacological Sciences (2022)

Monoclonal antibodies represent an exciting class of therapeutics against respiratory viral infections. Notwithstanding their specificity and affinity, the conventional parenteral administration is suboptimal in delivering antibodies for neutralizing activity in the airways due to the poor distribution of macromolecules to the respiratory tract. Inhaled therapy is a promising approach to overcome this hurdle in a noninvasive manner, while advances in antibody engineering have led to the development of unique antibody formats which exhibit properties desirable for inhalation. In this Opinion, we examine the major challenges surrounding the development of inhaled antibodies, identify knowledge gaps that need to be addressed and provide strategies from a drug delivery perspective to enhance the efficacy and safety of neutralizing antibodies against respiratory viral infections.
Confounders mediate AI prediction of demographics in medical imaging
Authors: Grant Duffy, Shoa L. Clarke, Matthew Christensen, Bryan He, Neal Yuan, Susan Cheng, David Ouyang
Journal: npj Digital Medicine (2022)

Abstract Deep learning has been shown to accurately assess “hidden” phenotypes from medical imaging beyond traditional clinician interpretation. Using large echocardiography datasets from two healthcare systems, we test whether it is possible to predict age, race, and sex from cardiac ultrasound images using deep learning algorithms and assess the impact of varying confounding variables. Using a total of 433,469 videos from Cedars-Sinai Medical Center and 99,909 videos from Stanford Medical Center, we trained video-based convolutional neural networks to predict age, sex, and race. We found that deep learning models were able to identify age and sex, while unable to reliably predict race. Without considering confounding differences between categories, the AI model predicted sex with an AUC of 0.85 (95% CI 0.84–0.86), age with a mean absolute error of 9.12 years (95% CI 9.00–9.25), and race with AUCs ranging from 0.63 to 0.71. When predicting race, we show that tuning the proportion of confounding variables (age or sex) in the training data significantly impacts model AUC (ranging from 0.53 to 0.85), while sex and age prediction was not particularly impacted by adjusting race proportion in the training dataset AUC of 0.81–0.83 and 0.80–0.84, respectively. This suggests significant proportion of AI’s performance on predicting race could come from confounding features being detected. Further work remains to identify the particular imaging features that associate with demographic information and to better understand the risks of demographic identification in medical AI as it pertains to potentially perpetuating bias and disparities.
Immunogenicity and safety of coadministration of COVID-19 and influenza vaccination
Authors: Isabell Wagenhäuser, Julia Reusch, Alexander Gabel, Anna Höhn, Thiên-Trí Lâm, Giovanni Almanzar, Martina Prelog, Lukas B. Krone, Anna Frey, Alexandra Schubert-Unkmeir, Lars Dölken, Stefan Frantz, Oliver Kurzai, Ulrich Vogel, Nils Petri, Manuel Krone
Journal: European Respiratory Journal (2022)

<b>Coadministration of seasonal quadrivalent influenza and COVID-19 booster vaccination is safe and does not increase vaccine-related side-effects, but may limit anti-SARS-CoV-2 antibody formation</b> https://bit.ly/3uKFUie
Phase‐Separated Liposomes Hijack Endogenous Lipoprotein Transport and Metabolism Pathways to Target Subsets of Endothelial Cells In Vivo
Authors: Gabriela Arias‐Alpizar, Panagiota Papadopoulou, Xabier Rios, Krishna Reddy Pulagam, Mohammad‐Amin Moradi, Roy Pattipeiluhu, Jeroen Bussmann, Nico Sommerdijk, Jordi Llop, Alexander Kros, Frederick Campbell
Journal: Advanced Healthcare Materials (2022)

Plasma lipid transport and metabolism are essential to ensure correct cellular function throughout the body. Dynamically regulated in time and space, the well-characterized mechanisms underpinning plasma lipid transport and metabolism offers an enticing, but as yet underexplored, rationale to design synthetic lipid nanoparticles with inherent cell/tissue selectivity. Herein, a systemically administered liposome formulation, composed of just two lipids, that is capable of hijacking a triglyceride lipase-mediated lipid transport pathway resulting in liposome recognition and uptake within specific endothelial cell subsets is described. In the absence of targeting ligands, liposome-lipase interactions are mediated by a unique, phase-separated ("parachute") liposome morphology. Within the embryonic zebrafish, selective liposome accumulation is observed at the developing blood-brain barrier. In mice, extensive liposome accumulation within the liver and spleen - which is reduced, but not eliminated, following small molecule lipase inhibition - supports a role for endothelial lipase but highlights these liposomes are also subject to significant "off-target" by reticuloendothelial system organs. Overall, these compositionally simplistic liposomes offer new insights into the discovery and design of lipid-based nanoparticles that can exploit endogenous lipid transport and metabolism pathways to achieve cell selective targeting in vivo.
Disparities and Trends in Genitourinary Cancer Incidence and Mortality in the USA
Authors: Elizabeth J. Schafer, Ahmedin Jemal, Daniel Wiese, Hyuna Sung, Tyler B. Kratzer, Farhad Islami, William L. Dahut, Karen E. Knudsen
Journal: European Urology (2022)

Previous studies have reported on incidence and mortality patterns for individual genitourinary cancers in the USA. However, these studies addressed individual cancer types rather than genitourinary cancers overall. To comprehensively examine disparities and trends in the incidence and mortality for the four major genitourinary cancers (bladder, kidney, prostate, and testis) in the USA. We obtained incidence data from the National Cancer Institute 22-registry Surveillance, Epidemiology and End Results (SEER) database and the US Cancer Statistics database (Centers for Disease Control and Prevention) and mortality data from the National Center for Health Statistics to examine cross-sectional and temporal trends in incidence and death rates stratified by sex, race/ethnicity, and county. Age-adjusted incidence and death rates were calculated using SEER*Stat software. Temporal trends were analyzed using Joinpoint regression for a two-sided significance level of p < 0.05. Incidence and mortality rates for bladder and kidney cancers were two to four times higher for men than for women. Among non-Hispanic White individuals, the highest incidence rates were found in the Northeast for bladder cancer and in Appalachia for kidney cancer, whereas the highest death rates for prostate cancer were found in the West. Incidence rates increased for cancers of the kidney and testis and for advanced-stage prostate cancer in almost all racial/ethnic populations and for bladder cancer in the American Indian/Alaska Native population. Death rates increased for testicular cancer in the Hispanic population and stabilized for prostate cancer among White and Asian American/Pacific Islander men after a steady decline since the early 1990s. Study limitations include misclassification of race/ethnicity on medical records and death certificates. We found persistent sociodemographic disparities and unfavorable trends in incidence or mortality for all four major genitourinary cancers. Future studies should elucidate the reasons for these patterns. In the USA, rates of cancer cases are increasing for kidney, testis, and advanced-stage prostate cancers in the overall population, and for bladder cancer in the American Indian/Alaska Native population. Differences in the rates by sex and race/ethnicity remain.
Dupuytren's disease: a localised and accessible human fibrotic disorder
Authors: Thomas B Layton, Lynn Williams, Jagdeep Nanchahal
Journal: Trends in Molecular Medicine (2022)

We review the biology of Dupuytren's disease (DD), a common localised fibrotic disorder of the hand. The disease develops through a complex interplay of genetic and environmental factors, and epigenetic signalling. The early-stage disease nodules comprise a complex milieu of stromal and immune cells which interact to promote disease development. Recently, inhibition of tumour necrosis factor (TNF) locally resulted in softening and a decrease in nodule size, potentially controlling disease progression. Unlike fibrotic disorders of the visceral organs, the easy access to tissue in DD patients enables dissection of the cellular landscape and molecular signalling pathways. In addition, the study of DD may have wider benefits in enhancing our understanding of less-accessible fibrotic tissues.
An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2
Authors: Katherine C. Barnett, Yuying Xie, Takanori Asakura, Dingka Song, Kaixin Liang, Sharon A. Taft-Benz, Haitao Guo, Shuangshuang Yang, Kenichi Okuda, Rodney C. Gilmore, Jennifer F. Loome, Thomas H. Oguin III, Gregory D. Sempowski, Scott H. Randell, Mark T. Heise, Yu Leo Lei, Richard C. Boucher, Jenny P.-Y. Ting
Journal: Cell Host & Microbe (2022)
Targeting inflammation to treat diabetic kidney disease: the road to 2030
Authors: Sandra Rayego-Mateos, Raul R Rodrigues-Diez, Beatriz Fernandez-Fernandez, Carmen Mora-Fernández, Vanessa Marchant, Javier Donate-Correa, Juan F. Navarro-González, Alberto Ortiz, Marta Ruiz-Ortega
Journal: Kidney International (2022)
Surgical gestures as a method to quantify surgical performance and predict patient outcomes
Authors: Runzhuo Ma, Ashwin Ramaswamy, Jiashu Xu, Loc Trinh, Dani Kiyasseh, Timothy N. Chu, Elyssa Y. Wong, Ryan S. Lee, Ivan Rodriguez, Gina DeMeo, Aditya Desai, Maxwell X. Otiato, Sidney I. Roberts, Jessica H. Nguyen, Jasper Laca, Yan Liu, Katarina Urbanova, Christian Wagner, Animashree Anandkumar, Jim C. Hu, Andrew J. Hung
Journal: npj Digital Medicine (2022)

How well a surgery is performed impacts a patient's outcomes; however, objective quantification of performance remains an unsolved challenge. Deconstructing a procedure into discrete instrument-tissue "gestures" is a emerging way to understand surgery. To establish this paradigm in a procedure where performance is the most important factor for patient outcomes, we identify 34,323 individual gestures performed in 80 nerve-sparing robot-assisted radical prostatectomies from two international medical centers. Gestures are classified into nine distinct dissection gestures (e.g., hot cut) and four supporting gestures (e.g., retraction). Our primary outcome is to identify factors impacting a patient's 1-year erectile function (EF) recovery after radical prostatectomy. We find that less use of hot cut and more use of peel/push are statistically associated with better chance of 1-year EF recovery. Our results also show interactions between surgeon experience and gesture types-similar gesture selection resulted in different EF recovery rates dependent on surgeon experience. To further validate this framework, two teams independently constructe distinct machine learning models using gesture sequences vs. traditional clinical features to predict 1-year EF. In both models, gesture sequences are able to better predict 1-year EF (Team 1: AUC 0.77, 95% CI 0.73-0.81; Team 2: AUC 0.68, 95% CI 0.66-0.70) than traditional clinical features (Team 1: AUC 0.69, 95% CI 0.65-0.73; Team 2: AUC 0.65, 95% CI 0.62-0.68). Our results suggest that gestures provide a granular method to objectively indicate surgical performance and outcomes. Application of this methodology to other surgeries may lead to discoveries on methods to improve surgery.